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The genetic code is the set of rules used by living cells to translate information encoded within genetic material into proteins. Translation is accomplished by the ribosome, which links proteinogenic amino acids in an order specified by messenger RNA (mRNA), using transfer RNA (tRNA) molecules to carry amino acids and to read the mRNA three nucleotides at a time. The genetic code is highly similar among all organisms and can be expressed in a simple table with 64 entries.
In molecular biology, a stop codon is a codon that signals the termination of the translation process of the current protein. Most codons in messenger RNA correspond to the addition of an amino acid to a growing polypeptide chain, which may ultimately become a protein; stop codons signal the termination of this process by binding release factors, which cause the ribosomal subunits to disassociate, releasing the amino acid chain.
Molecular evolution is the process of change in the sequence composition of cellular molecules such as DNA, RNA, and proteins across generations. The field of molecular evolution uses principles of evolutionary biology and population genetics to explain patterns in these changes. Major topics in molecular evolution concern the rates and impacts of single nucleotide changes, neutral evolution vs. natural selection, origins of new genes, the genetic nature of complex traits, the genetic basis of speciation, evolution of development, and ways that evolutionary forces influence genomic and phenotypic changes.
In molecular biology, a reading frame is a way of dividing the sequence of nucleotides in a nucleic acid molecule into a set of consecutive, non-overlapping triplets. Where these triplets equate to amino acids or stop signals during translation, they are called codons.
Indel is a molecular biology term for an insertion or deletion of bases in the genome of an organism. It is classified among small genetic variations, measuring from 1 to 10 000 base pairs in length, including insertion and deletion events that may be separated by many years, and may not be related to each other in any way. A microindel is defined as an indel that results in a net change of 1 to 50 nucleotides.
The start codon is the first codon of a messenger RNA (mRNA) transcript translated by a ribosome. The start codon always codes for methionine in eukaryotes and Archaea and a N-formylmethionine (fMet) in bacteria, mitochondria and plastids. The most common start codon is AUG.
MT-ATP6 is a mitochondrial gene with the full name 'mitochondrially encoded ATP synthase membrane subunit 6' that encodes the ATP synthase Fo subunit 6. This subunit belongs to the Fo complex of the large, transmembrane F-type ATP synthase. This enzyme, which is also known as complex V, is responsible for the final step of oxidative phosphorylation in the electron transport chain. Specifically, one segment of ATP synthase allows positively charged ions, called protons, to flow across a specialized membrane inside mitochondria. Another segment of the enzyme uses the energy created by this proton flow to convert a molecule called adenosine diphosphate (ADP) to ATP. Mutations in the MT-ATP6 gene have been found in approximately 10 to 20 percent of people with Leigh syndrome.
Ribosomal frameshifting, also known as translational frameshifting or translational recoding, is a biological phenomenon that occurs during translation that results in the production of multiple, unique proteins from a single mRNA. The process can be programmed by the nucleotide sequence of the mRNA and is sometimes affected by the secondary, 3-dimensional mRNA structure. It has been described mainly in viruses, retrotransposons and bacterial insertion elements, and also in some cellular genes.
An expanded genetic code is an artificially modified genetic code in which one or more specific codons have been re-allocated to encode an amino acid that is not among the 22 common naturally-encoded proteinogenic amino acids.
Mitochondrial translational release factor 1, also known as MTRF1 is a human gene.
A codon table can be used to translate a genetic code into a sequence of amino acids. The standard genetic code is traditionally represented as an RNA codon table, because when proteins are made in a cell by ribosomes, it is messenger RNA (mRNA) that directs protein synthesis. The mRNA sequence is determined by the sequence of genomic DNA. In this context, the standard genetic code is referred to as translation table 1. It can also be represented in a DNA codon table. The DNA codons in such tables occur on the sense DNA strand and are arranged in a 5′-to-3′ direction. Different tables with alternate codons are used depending on the source of the genetic code, such as from a cell nucleus, mitochondrion, plastid, or hydrogenosome.
Agmatidine (2-agmatinylcytidine, symbol C+ or agm2C) is a modified cytidine present in the wobble position of the anticodon of several archaeal AUA decoding tRNAs. Agmatidine is essential for correct decoding of the AUA codon in many archaea and is required for aminoacylation of tRNAIle2 with isoleucine.
Mitochondrial translational release factor 1-like is a protein that in humans is encoded by the MTRF1L gene.
The pterobranchia mitochondrial code is a genetic code used by the mitochondrial genome of Rhabdopleura compacta (Pterobranchia). The Pterobranchia are one of the two groups in the Hemichordata which together with the Echinodermata and Chordata form the three major lineages of deuterostomes. AUA translates to isoleucine in Rhabdopleura as it does in the Echinodermata and Enteropneusta while AUA encodes methionine in the Chordata. The assignment of AGG to lysine is not found elsewhere in deuterostome mitochondria but it occurs in some taxa of Arthropoda. This code shares with many other mitochondrial codes the reassignment of the UGA STOP to tryptophan, and AGG and AGA to an amino acid other than arginine. The initiation codons in Rhabdopleura compacta are ATG and GTG.
The yeast mitochondrial code is a genetic code used by the mitochondrial genome of yeasts, notably Saccharomyces cerevisiae, Candida glabrata, Hansenula saturnus, and Kluyveromyces thermotolerans.
The bacterial, archaeal and plant plastid code is the DNA code used by bacteria, archaea, prokaryotic viruses and chloroplast proteins. It is essentially the same as the standard code, however there are some variations in alternative start codons.
The invertebrate mitochondrial code is a genetic code used by the mitochondrial genome of invertebrates.
The ambush hypothesis is a hypothesis in the field of molecular genetics that suggests that the prevalence of “hidden” or off-frame stop codons in DNA selectively deters off-frame translation of mRNA to save energy, molecular resources, and to reduce strain on biosynthetic machinery by truncating the production of non-functional, potentially cytotoxic protein products. Typical coding sequences of DNA lack in-frame internal stop codons to avoid the premature reduction of protein products when translation proceeds normally. The ambush hypothesis suggests that kinetic, cis-acting mechanisms are responsible for the productive frameshifting of translational units so that the degeneracy of the genetic code can be used to prevent deleterious translation. Ribosomal slippage is the most well described mechanism of translational frameshifting where the ribosome moves one codon position either forward (+1) or backward (-1) to translate the mRNA sequence in a different reading frame and thus produce different protein products.
The ascidian mitochondrial code is a genetic code found in the mitochondria of Ascidia.
The Cephalodiscidae mitochondrial code is a genetic code used by the mitochondrial genome of Cephalodiscidae (Pterobranchia). The Pterobranchia are one of the two groups in the Hemichordata which together with the Echinodermata and Chordata form the major clades of deuterostomes.
References
- This article contains public domain text from the NCBI page compiled by Andrzej (Anjay) Elzanowski and Jim Ostell. [9]
- ↑ S. Osawa, T. Ohama, T. H. Jukes and K. Watanabe (September 1989). "Evolution of the mitochondrial genetic code. I. Origin of AGR serine and stop codons in metazoan mitochondria". J Mol Evol. 29 (3): 202–7. Bibcode:1989JMolE..29..202O. doi:10.1007/bf02100203. PMID 2506356. S2CID 21051869.
{{cite journal}}: CS1 maint: multiple names: authors list (link) - ↑ R J Temperley; R Richter; S Dennerlein; R N Lightowlers; Z M Chrzanowska-Lightowlers (January 2010). "Hungry codons promote frameshifting in human mitochondrial ribosomes". Science. 327 (5963): 301. Bibcode:2010Sci...327..301T. doi:10.1126/science.1180674. PMID 20075246. S2CID 206522983.
- ↑ Temperley, R. J.; Wydro, M; Lightowlers, R. N.; Chrzanowska-Lightowlers, Z. M. (2010). "Human mitochondrial mRNAs--like members of all families, similar but different". Biochimica et Biophysica Acta (BBA) - Bioenergetics. 1797 (6–7): 1081–5. doi:10.1016/j.bbabio.2010.02.036. PMC 3003153 . PMID 20211597.
- ↑ W. R. Hou, Y. Chen, X. Wu, J. C. Hu, Z. S. Peng, J. Yang, Z. X. Tang, C. Q. Zhou, Y. M. Li, S. K. Yang, Y. J. Du, L. L. Kong, Z. L. Ren, H. Y. Zhang and S. S. Shuai (December 2006). "A complete mitochondrial genome sequence of Asian black bear Sichuan subspecies (Ursus thibetanus mupinensis)". Int J Biol Sci. 3 (2): 85–90. doi:10.7150/ijbs.3.85. PMC 1752227 . PMID 17205108.
{{cite journal}}: CS1 maint: multiple names: authors list (link) - ↑ Oh, D. J.; Kim, J. Y.; Lee, J. A.; Yoon, W. J.; Park, S. Y.; Jung, Y. H. (2007). "Complete mitochondrial genome of the rabbitfish Siganus fuscescens (Perciformes, Siganidae)". DNA Sequence. 18 (4): 295–301. doi:10.1080/10425170701248525. PMID 17541835. S2CID 38458668.
- ↑ Ki, J. S.; Hwang, D. S.; Park, T. J.; Han, S. H.; Lee, J. S. (2009). "A comparative analysis of the complete mitochondrial genome of the Eurasian otter Lutra lutra (Carnivora; Mustelidae)". Molecular Biology Reports. 37 (4): 1943–55. doi:10.1007/s11033-009-9641-0. PMID 19757186. S2CID 24233602.
- ↑ Nakamoto T (March 2009). "Evolution and the universality of the mechanism of initiation of protein synthesis". Gene. 432 (1–2): 1–6. doi:10.1016/j.gene.2008.11.001. PMID 19056476.
- ↑ P. Desjardins & R. Morais (February 1991). "Nucleotide sequence and evolution of coding and noncoding regions of a quail mitochondrial genome". J Mol Evol. 32 (2): 153–161. Bibcode:1991JMolE..32..153D. doi:10.1007/bf02515387. PMID 1706782. S2CID 1974138.
- ↑ The Genetic Codes